Comments (2)
Hi @bnwlf.
Test data (and corresponding references) in https://github.com/nf-core/test-datasets is in the sarek branch.
Using the test profile will use the specific test config file: https://github.com/nf-core/sarek/blob/master/conf/test.config
Input file is mainly this tsv file: https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/tsv/tiny-manta-https.tsv that contain https path to the different fastq pairs.
In this repository there is all the other tsv files than can be used for testing.
If the file end with -https.txt
path to fastq/bam is with https otherwise, it's assuming you used git clone to download the test-datasets repo in the data folder within the current directory.
Several tests are actually run with GitHub Actions (cf https://github.com/nf-core/sarek/blob/master/.github/workflows/ci.yml).
But the Nextflow command that I generally use to test is nextflow run nf-core/sarek -profile test,docker
(it tests preprocessing, which is I think the critical part).
To have a more complete experience, you can add --tools Strelka,Manta,HaplotypeCaller
I hope I replied to your questions.
Don't hesitate if you have need more clarification.
from test-datasets.
It will be good also to add information about that in the nf-core/sarek repo in the troubleshooting section of the usage documentation
from test-datasets.
Related Issues (20)
- Remove ambiguous bases from MAG test data
- Clean up bam/cram homo_sapiens files for modules tests data
- Including indexing files for new module verifybamid HOT 3
- Split modules vs pipeline test module
- Re-run tests of all affected modules when a given test-data file is updated/modified
- Add sets of species nucleotide.fasta or protein.fasta for orthology analysis
- Add bed file for ONCOCNV
- Add cyano nucleotide taxonomy to phyloplace test data
- Rename spatialomics to imaging for modules branch HOT 2
- Add test datasets for imaging modules HOT 3
- Add new test data for sammyseq
- Add Unsorted text data
- Move unsorted data into the generic data dir
- refactor test data for `cellranger` modules HOT 1
- Add database subsampled data for snpSift module (dbnsnpf) HOT 1
- fix missing `cellranger` data summary info HOT 1
- cellranger data refactor broke tests for non-cellranger modules
- Pipedreams
- Use git-lfs
- Use version tags on branches HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from test-datasets.